http://www.wmd-lab.org/positions.htm

University of California
Campus: San Diego (http://www.ucsd.edu)

Academic Department/Research Unit:
San Diego Supercomputer Center (http://www.sdsc.edu)

Research Discipline:
Computational Molecular Biology/Chemistry, High Performance Computing

Description:
A postdoctoral position in computational molecular biology is available
immediately within the group of Prof Ross Walker at the San Diego
Supercomputer Center. This will involve close collaboration with researchers
at UCSD, Cornell, University of Michigan and the National Renewable Energy
Laboratory to carry out research in the field of algorithm and method
development for Molecular Dynamics Simulations.

The research focus of the group is advanced Molecular Dynamics (MD)
simulations and related method development. It includes the development of
efficient algorithms for accurate and parallel computation of quantum
mechanical and hybrid quantum mechanical/molecular mechanical (QM/MM) MD
simulations; comprehensive force field development for simulation of complex
phospholipid membranes; improved sampling techniques for classical and QM/MM
MD simulations; GPU acceleration of MD simulations; the development of novel
approaches for analysis of large scale and long time length MD simulation
trajectories; approaches to parallel post-processing and on the fly MD
analysis; the use of MD simulation techniques for studying protein
reactivity including elucidation of the activation pathways and, specific to
this project, studies of cellulose degrading enzymes for use in bio-fuel
production.

The successful candidate will interact with the developers of the AMBER and
CHARMM software packages to develop improved techniques for modeling enzymes
involved in cellulose degradation although the techniques developed will be
of general benefit to all MD researchers. This work will include the
development, optimization and validation of highly scalable algorithms and
software addressing complex MD simulation techniques that go beyond the
traditional explicit solvent PME approaches that most parallel MD packages
currently implement. This will include development for both traditional
highly parallel architectures and also emerging technologies such as GPUs
and other accelerator technologies. While the focus will mostly be on
classical MD techniques there is opportunity, for a candidate with
additional QM/MM experience to work on extending the QM/MM functionality of
the AMBER software. The incumbent will have access to SDSC, DOE and NSF
supercomputer resources including some of the world's most powerful
machines. Occasional travel may be required including visits to the
collaborating sites approximately 2 to 3 times per year and presentation of
results at scientific conferences.

Skills and Knowledge Required:
The applicant should have, or expect to shortly receive, a Ph.D. in
Computational Biology, Computational Chemistry, Computational Life Sciences
or relevant disciplines as well as research experience in computational
molecular biology, and strong computer programming skills, including Fortran
95 and C/C++ and knowledge of molecular biology, protein structure and
molecular dynamics. Applicants with Ph.D.'s in Computer Science backgrounds
will also be considered if they have experience in molecular dynamics
simulations or related disciplines. Experience in high performance
computing, molecular dynamics and parallel (MPI) or GPU programming (CUDA)
is also extremely desirable. Applicants should enjoy working on challenging
and exciting projects together with a team of international experts.

Location:
Nestled along the Pacific Ocean on 1,200 acres of coastal woodland, with
year round summer, just steps from the beach and minutes from beautiful
downtown La Jolla, UC San Diego is a preeminent university in the country
providing an excellent environment for research in computational biology,
computer science, biochemistry, bioengineering, medicine, as well as
interdisciplinary research. The successful candidate will reside in the new
building of San Diego Supercomputer Center on the main campus of UCSD.

Salary/Stipend Information:
Commensurate with NIH Guidelines.

Benefits:
This position qualifies for Full Postdoctoral Benefits - see
http://research.ucsd.edu/postdoc/benefits.aspx for further information.

Procedure to Apply:
Interested individuals should e-mail their curriculum vitae, a cover letter
stating research interests and career goals and the names, telephone
numbers, and e-mail addresses of three references to Prof. Ross C. Walker at
rcw_at_sdsc.edu. 

Position Closing Date:
Open Until Filled.

Appointment Length/Period:
Initial appointment for one year, with the possibility of renewals.

For more information or to apply, please contact:
Ross C. Walker, Phd
rcw_at_sdsc.edu

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